Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

-Original Message- > From: CCP4 bulletin board On Behalf Of Gerard Bricogne > Sent: Friday, April 26, 2024 11:47 AM > To: CCP4BB@JISCMAIL.AC.UK > Subject: [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG > > EXTERNAL EMAIL: Use caution before replying, clicking links, and open

Re: [ccp4bb] add ligand with AceDRG

Use the search tab at the RCSB web site, type in a 3 letter code, and if it has been used for a ligand then it will appear as a Chemical Component. Thanks to Phil, I am on vacation in Mexico and cut and pasting URLs is a pain on an iPhone. Diana Sent from my iPhone On Apr 26, 2024, at 9:07 

Re: [ccp4bb] [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG

board On Behalf Of Gerard Bricogne Sent: Friday, April 26, 2024 11:47 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [EXTERNAL] Re: [ccp4bb] add ligand with AceDRG EXTERNAL EMAIL: Use caution before replying, clicking links, and opening attachments. Dear Oliver and CCP4BB readers, This obsoleted LIG came

Re: [ccp4bb] add ligand with AceDRG

..@durham.ac.uk > > <mailto:stefanie.freitag-p...@durham.ac.uk> > > From: CCP4 bulletin board > <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of FREITAG-POHL, STEFANIE > > > <mailto:stefanie.freitag-p...@durham.ac.uk>> > > Sent: 25 April 2024 13:01 > >

Re: [ccp4bb] add ligand with AceDRG

gt; on behalf of FREITAG-POHL, STEFANIE > <mailto:stefanie.freitag-p...@durham.ac.uk>> > Sent: 25 April 2024 13:01 > To: CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > mailto:CCP4BB@JISCMAIL.AC.UK>> > Subject: [ccp4bb] add ligand with AceDRG > > [EXT

Re: [ccp4bb] add ligand with AceDRG

Thanks for the feedback, I will let PDBe developers know that this is causing confusion and that LIG should not return results. Kind regards, Deborah On 26/04/2024 16:11, Garib Murshudov wrote: On this website: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ If you search for LIG it returns a

Re: [ccp4bb] add ligand with AceDRG

Indeed, as Diana points out: PDB's own components.cif defines LIG as: _chem_comp.id LIG _chem_comp.name "3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.]PYRAZOLE" _chem_comp.type NON-POLYMER _chem_comp.pdbx_type HETAIN _chem_comp.formula "C15 H11 N3" So they probably should fix that. Also that

Re: [ccp4bb] add ligand with AceDRG

On this website: https://www.ebi.ac.uk/pdbe-srv/pdbechem/ If you search for LIG it returns a ligand. With small letters it says: The chemical component you are trying to view (LIG) has been obsoleted. You have been redirected to the component

Re: [ccp4bb] add ligand with AceDRG

Hi Diana, Could you please clarify where you are searching? LIG is obsolete and definitely not in use. Cheers, Deborah On 26/04/2024 15:40, Diana Tomchick wrote: But I think that is a mistake, if you search for LIG in the PDB, it brings up a definite ligand that has that 3-letter code.

Re: [ccp4bb] add ligand with AceDRG

But I think that is a mistake, if you search for LIG in the PDB, it brings up a definite ligand that has that 3-letter code. Diana Sent from my iPhone On Apr 26, 2024, at 8:04 AM, Deborah Harrus wrote:  Dear all, Just to clarify, "LIG" is also a reserved code, so it's safe to use. See

Re: [ccp4bb] add ligand with AceDRG

Dear all, Just to clarify, "LIG" is also a reserved code, so it's safe to use. See https://www.wwpdb.org/news/news?year=2023#656f4404d78e004e766a96c6 Kind regards, Deborah Harrus PDBe On 25/04/2024 16:04, Diana Tomchick wrote: The PDB has reserved the following codes for unknown ligands:

Re: [ccp4bb] add ligand with AceDRG

Thank you Paul. I did not think about it. Stefanie, could you please send the log file to me? Regards Garib > On 26 Apr 2024, at 14:17, Paul Emsley wrote: > > > On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote: >> >> >> >> I have trouble adding a ligand with AceDRG in CCP4i2 into my

Re: [ccp4bb] add ligand with AceDRG

On 25/04/2024 13:01, FREITAG-POHL, STEFANIE wrote: I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement: I put in a smilesstring and the ligand is written ok, but since I can only chose already 'taken' 3-letter-codes the refinement always crashes as there is a clash with

Re: [ccp4bb] add ligand with AceDRG

MAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> mailto:CCP4BB@JISCMAIL.AC.UK>> Subject: [ccp4bb] add ligand with AceDRG [EXTERNAL EMAIL] Hi all, I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement: I put in a smilesstring and the ligand is written ok, but since I can

Re: [ccp4bb] add ligand with AceDRG

tag-p...@durham.ac.uk <mailto:stefanie.freitag-p...@durham.ac.uk> > From: CCP4 bulletin board <mailto:CCP4BB@JISCMAIL.AC.UK>> on behalf of FREITAG-POHL, STEFANIE > <mailto:stefanie.freitag-p...@durham.ac.uk>> > Sent: 25 April 2024 13:01 > To: CCP4BB@JISCMAIL.AC.UK <mailto

Re: [ccp4bb] add ligand with AceDRG

334 2596 stefanie.freitag-p...@durham.ac.uk<mailto:stefanie.freitag-p...@durham.ac.uk> From: CCP4 bulletin board on behalf of FREITAG-POHL, STEFANIE Sent: 25 April 2024 13:01 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] add ligand with AceDRG [EXTERNAL EMA

Re: [ccp4bb] add ligand with AceDRG

The PDB has reserved the following codes for unknown ligands: DRG INH 01 - 99 Using one of these should not cause you the described problems. I successfully used 99 just last week. If you try to use 999 or LIG these will not work, there are ligands assigned to those codes. Diana Sent

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, If you could run from command-lines, it will be easy to solve this problem. try from command-line, type acedrg -i "your_smiles_string" -r your_3_letter_code -o your_out_file_name For example, acedrg -i "C[C@@H](C(=O)O)N" -r UNL -o UNL You will get a file called UNL.cif, which

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, Why can you only use "taken" three letter codes? In the "output monomer" box, you should be able to enter whatever you'd like for the "Three letter code for output monomer". In the attached image, this is shown as "DRG" but can be changed to any 3 letter code of your choice.

Re: [ccp4bb] add ligand with AceDRG

Hi Stefanie, Can you manually edit the restraints file using TextEdit and find and replace and the pdb file of course? Other option is to use Grade or Grade2 and the smiles string if you have this software installed. I often find this easier than ccp4i2. Best regards and good luck! Maria >

Re: [ccp4bb] add ligand with AceDRG

board on behalf of FREITAG-POHL, STEFANIE Sent: 25 April 2024 13:01 To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] add ligand with AceDRG External Sender: Use caution. Hi all, I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement: I put in a smilesstring and the ligand

[ccp4bb] add ligand with AceDRG

Hi all, I have trouble adding a ligand with AceDRG in CCP4i2 into my refinement: I put in a smilesstring and the ligand is written ok, but since I can only chose already 'taken' 3-letter-codes the refinement always crashes as there is a clash with existing library entries. Is there any way